2RH6 | pdb_00002rh6

Structure of Xac NPP for evaluation of refinement methodology

• PDB DOI: https://doi.org/10.2210/pdb2RH6/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas citri subsp. citri 306
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-06 Released: 2007-10-30 
• Deposition Author(s): Zalatan, J.G., Fenn, T.D., Brunger, A.T., Hershlag, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.211 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystallographic Goodness of Fit: A New Treatment of Model Complexity

Fenn, T.D., Pozharski, E., Wilson, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.79 kDa 
• Atom Count: 6,809 
• Modeled Residue Count: 764 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphodiesterase-nucleotide pyrophosphatase	A, B	393	Xanthomonas citri subsp. citri 306	Mutation(s): 0  EC: 3.6.1.9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	E [auth A], H [auth B], I [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.211 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.049	α = 90
b = 78.62	β = 90
c = 129.953	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Zalatan, J.G., Fenn, T.D., Brunger, A.T., Hershlag, D.

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary